covid-19 guidance for sampling and laboratory investigations · 2020-04-03 · links to relevant...
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COVID-19 Guidance for sampling and laboratory investigations Version 7.2
Publication date: 17/04/ 2020
Health Protection Scotland
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Version history
Version Date Summary of changes
v0.2 23/01/2020 First publication
v2.0 01/02/2020
Additional information added to introduction
Removed line stating that CL3 facilities are available in all microbiology laboratories
Updated to align with PHE guidance
Added information about laboratory reporting of results to HPS
Throughout text: limited changes to wording for clarification
New nomenclature and new case definition
V3.0 02/02/2020 Updated contact details (appendix 1)
V4.0 04/02/2020 Updated information about POCT in line with PHE guidance
Updated PHE Colindale packaging requirements
V5.0 07/02/20 Amended to align with updated case definition and contact definition issued by PHE on 06/02/20
V5.1 07/02/20 Small amendment to contact definition
V6.0 10/02/20 Updated to align sample types and with PHE guidance issued by PHE 06/02/20
Amended throughout to clarify correct processes due to the roll out of laboratory testing in Scotland
V6.1 15/02/2020 Changes to formatting of results section to improve clarity
Link to request form for WOSSVC added
Amendment to epidemiological criteria in possible case definition to include transit through an at risk area
HPS number removed from local HPT contact list
Links to relevant HPS guidance documents added
Added comment that pneumatic tubes should not be used for sample transport
Updated nomenclature to SARS-CoV-2 for the virus and COVID-19 for the disease
Updated PHE hyperlinks in line with updated nomenclature.
Added link to PHE packaging video.
V6.2 26/02/2020 Updated reporting results section to include reporting of presumptive positive information
Removed Actions for WOSSVC/Edinburgh SVC from reporting results section
Updated link to PHE packaging video
V6.3 11/03/2020 Change to case definition
Removed information about confirmation of positives at Colindale, including change from presumptive positive to confirmed positive.
Changed information about containment level in line with updated PHE guidance
V7.1 26/03/2020 Remove case definition and insert link to HPT guidance, Primary care guidance and Secondary Care guidance where this information can be found
Changes to align with changes to where samples will be tested
Update which samples will be tested to be clearer
Update IPC guidance link
Health Protection Scotland
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Version Date Summary of changes
Update transport requirements
Include request to add epidemiology codes to clinical details
Add link to PHE prioritisation document
Added contact details for laboratories.
V7.2 17/04/20 Testing in care home settings
Link added to IPC step down criteria
Health Protection Scotland
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Contents
Introduction .............................................................................................................................. 4
Case definition ......................................................................................................................... 4
Approach to sampling .............................................................................................................. 5
Sample requirements for COVID-19 testing ......................................................................... 6
Additional samples which may be required .......................................................................... 6
Requirements for the request form ....................................................................................... 7
Requirements for sample transport ...................................................................................... 7
Results of testing ..................................................................................................................... 8
Actions for the microbiology laboratory................................................................................. 8
Actions for local Health Protection team ............................................................................... 8
Guidance for microbiologists/virologists ................................................................................... 9
Samples for routine microbiology testing .............................................................................. 9
Samples for SARS-CoV-2 testing ......................................................................................... 9
Appendix 1 – Contacts in local Health Protection teams ........................................................ 10
Appendix 2 – Contacts in local microbiology laboratories ...................................................... 11
Health Protection Scotland
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Introduction
Novel coronavirus (COVID-19) is a new strain of coronavirus first identified in Wuhan, China.
Clinical presentation may range from mild-to-moderate illness to pneumonia or severe acute
respiratory infection.
It has been announced by the UK/Scottish Government that as of 16 March anyone
developing symptoms consistent with COVID-19, however mild, should stay at home for 7
days from the onset of symptoms as per existing advice. In addition, it is now recommended
that anyone living in the same household as a symptomatic person should self-isolate for 14
days. Information on COVID-19, including advice for people who are symptomatic and their
households, can be found on NHS Inform.
Additional measures are recommended to help reduce the spread of COVID-19 and to
protect people at increased risk of severe illness. Information on these can be found on NHS
Inform.
Case definition
For the most updated case definition please refer to the following document: HPS Guidance
for Secondary Care.
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Approach to sampling
Sampling should be arranged for individuals admitted to hospital with suspected
COVID-19. Further information can be found in the HPS Secondary Care Guidance.
Samples may also be taken for other reasons, for example occupational health or to
inform health protection management e.g. for an outbreak within a closed setting.
Outbreak guidance states that the first 5 symptomatic residents in a care home setting should be tested to provide confirmation of an outbreak of COVID-19. On 15 April 2020 the Scottish Government announced the expansion of testing to include all care home residents who develop symptoms. Therefore Scotland will move to a system where any symptomatic patient in a care home will be clinically assessed and, where appropriate, offered testing for COVID-19. Samples may also be taken for other reasons, for example occupational health or to inform health protection management e.g. for an outbreak within a closed setting other than a care home.
Sampling for Key Workers should be performed according to the testing approach laid out by
your health board, based on Scottish Government Guidance for Health Boards: Testing
for COVID-19 Infection to Enable Key Workers to Return to Work.
Regular liaison with local virology/microbiology departments is important to ensure that
appropriate specimens are taken to establish the diagnosis and sufficient capacity is
available. The local laboratory will process and refer these samples to a referral laboratory by
category B transport if required.
All samples should be collected and processed in line with:
4 Nations Guidance: COVID-19: Guidance for Infection Prevention and Control in Healthcare settings
PHE Guidance: COVID-19: safe handling and processing for laboratories
HPS Guidance: COVID-19: Obtaining an upper respiratory diagnostic sample
Point of care tests, including blood gas analysis, should only be undertaken if a local
risk assessment has been completed and shows it can be undertaken safely.
Where clinically indicated, samples for routine microbiology and virology testing should be
collected and tested according to local protocols. It is essential to inform the laboratory
before samples are sent, and ensure that specimen request forms are clearly marked with
the relevant clinical and epidemiological history.
Health Protection Scotland
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There are currently no additional sample storage requirements beyond local laboratory
practice.
Sample requirements for COVID-19 testing
Upper respiratory tract sample(s):
o a viral nose swab AND a viral throat swab in one collection tube OR
o single swab used for throat then nose in one collection tube OR
o a nasopharyngeal aspirate in a universal transport pot.
Lower respiratory tract sample, if obtainable i.e. sputum in a universal container.
If the patient is admitted to hospital, a sample for serology should be collected at the
same time as other samples collected for primary diagnostic testing for COVID-19. A 5
ml serum tube is required. For children <12 years, 1mL is acceptable. Where a
baseline serum sample is collected a convalescent sample will be required 14-
60 days following the acute sample. Clarification is being sought on the
collection of the convalescent sample, and further update will follow when
available.
Additional samples which may be required
Samples for repeat testing
o In certain circumstances, repeat sampling may be required; the testing laboratory will contact the requesting clinician if this is indicated.
Samples for monitoring confirmed COVID-19
o Sequential sampling may be required to monitor the progress of confirmed SARS-CoV-2 infection in secondary care, decided on a case-by-case basis. This should be performed in line with HPS COVID-19 - guidance for stepdown of infection control precautions and discharging COVID-19 patients from hospital to residential settings
Samples for outbreaks in closed and residential settings
o The name of the facility/ward and the date of the first case must be added to the clinical details in order to identify this as an outbreak sample (the date is required in order to differentiate between potential sequential outbreaks)
o In large outbreaks, in non-care home settings it may not be possible to test all samples. The testing laboratory will therefore test the first 5 samples submitted under each incident log as routine. Any further testing within the outbreak would be by discussion with the duty virologist at the laboratory only.
Health Protection Scotland
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Requirements for the request form
Please ensure that the category code listed below is included in the clinical details section of
the request form for the sample types below. Codes are not required for other sample types.
COVID Cat: SER GP sentinel samples.
COVID Cat: OCH Samples from individuals being tested for occupational reasons e.g. health care worker or household index case of a health care worker.
COVID Cat: ICU Patients receiving level 3 care.
Important points about sample-labelling and request forms:
each sample must be labelled with ID, date of birth and type of sample;
paperwork (request forms) should NOT be placed in the bag with the sample container
request form must include a contact phone number for sharing of results
samples without appropriate paperwork will not be tested
Requirements for sample transport
All samples should be packaged and transported in accordance with Category B
transportation regulations. UN 3373 packaging must be used for sample transport. If
required, transport requirements should be discussed with the specialist virology laboratory.
Specific requirements for sample packaging can be accessed at: COVID-19: packaging of
COVID-19 samples for referral to regional testing labs.
If moving samples within the same hospital, it is sufficient to double bag samples, which
should be transported by an appropriate person who is aware of the nature of the sample.
Health Protection Scotland
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Results of testing
Results of testing will be provided by the testing laboratory.
Patient management and public health action (as required) should be taken as soon as
a confirmed positive or presumptive positive result is available.
If another pathogen is identified, this does not rule out SARS-CoV-2 co-infection.
Actions for the microbiology laboratory
Positive results should be shared urgently with the requesting clinician and the local Health Protection team. In a secondary care setting positive results should also be urgently shared with the infection prevention and control team.
As a minimum, the laboratory should communicate ALL results to:
o The requesting clinician: If positive result note that screening assay has resulted in SARS-Cov-2 detection and to ensure the patient is being managed in line with COVID-19: Guidance for Infection Prevention and Control in Healthcare settings.
o The local Health Protection team (Appendix 1): Further guidance for HPT is available on the HPS website: HPS Guidance for Health Protection teams.
o Health Protection Scotland
o In a secondary care setting both positive and negative result should also be shared with the infection prevention and control team.
Actions for local Health Protection team
The local Health Protection Team should refer to HPS Guidance for Health Protection
teams.
Health Protection Scotland
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Guidance for microbiologists/virologists
Clinical laboratories should perform their own risk assessments for handling biological
specimens from patients with suspected or confirmed COVID-19 taking into account the
guidance outlined in:
COVID-19: Guidance for Infection Prevention and Control in Healthcare settings – 4 Nations Guidance
COVID-19: safe handling and processing for laboratories – PHE guidance
Laboratory algorithm: Algorithm summarising sampling and laboratory investigations for SARS-CoV-2
COVID-19 is a notifiable disease and SARS-CoV-2 is a notifiable organism under the
Public Health etc (Scotland) Act 2008, as outlined in a letter from the CMO.
An overview of the laboratory testing process for diagnostic samples can be seen in the HPS
algorithm: testing for SARS-CoV-2 in Scotland.
Samples for routine microbiology testing
Microbiological samples for tests performed locally will need to be handled at the appropriate
biological containment level. Further information about safe sample handling is available in
the PHE Guidance: COVID-19: safe handling and processing for laboratories specific for
SARS-CoV-2.
Testing should be performed where clinically indicated, in line with local arrangements
including referral where necessary.
Note that it is the responsibility of the treating centre to arrange investigations for pathogens
other than SARS-CoV-2.
Samples for SARS-CoV-2 testing
Please note that during periods of significant demand, samples may be prioritised as
described in PHE Guidance: Priority of SARS-CoV-2 (COVID-19) testing during periods
of significant demand.
These samples may also be tested using a routine respiratory virus panel as per current local
arrangements, however as the epidemic progresses, increasingly laboratories may need to
narrow the repertoire of testing. For patients of clinical concern additional test requirements
should be discussed with your local laboratory.
Health Protection Scotland
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Appendix 1 – Contacts in local Health Protection teams
Organisation Office Hours Telephone Number
Out of Hours Telephone Number
Ayrshire and Arran 01292 885858 01563 521 133
Crosshouse Hospital switchboard
Borders 01896 825560 01896 826 000
Borders General switchboard
Dumfries and Galloway 01387 272 724 01387 246 246
Fife 01592 226435 01592 643355
Victoria Hospital switchboard
Forth Valley 01786 457 283 Ask for CPHM on call
01324 566000 Ask for CPHM on call
Grampian 01224 558520 0345 456 6000
Greater Glasgow & Clyde 0141 201 4917 0141 211 3600
Gartnavel switchboard
Highland 01463 704886 01463 704000
Raigmore switchboard
Lanarkshire 01698 858232 01236 748 748
Monklands switchboard
Lothian 0131 465 5429/5422 0131 536 1000
Edinburgh Royal switchboard
Orkney 01856 888034 01856 888 000
Balfour Hospital switchboard
Shetland 01595 743340 01595 743000
Gilbert Bain switchboard
Tayside 01382 596 976/987 01382 660111
Ninewells switchboard
Western Isles 01851 704704 01851 708033
Ayrshire and Arran 01292 885858 01563 521 133
Crosshouse Hospital switchboard
Borders 01896 825560 01896 826 000
Borders General switchboard
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Appendix 2 – Contacts in local microbiology laboratories
Organisation Laboratory contact details
Ayrshire & Arran 01563 827420
Borders 01896 826250 01896 826258
Dumfries & Galloway 01387 241560
Fife 01592 648169
Forth Valley 01324 566692
Grampian 01224 552444
GGC
Virology: 0141 201 8721
Out of hours: 0141 211 4000 (ask for on-call virologist)
Email: [email protected]
Golden Jubilee 0141 951 5931
Highland 01463 704206
01463 704207
Lanarkshire (Wishaw) 01698 366405
Lothian
Virology: 0131 536 3373 (Option 2)
Out of hours: 0131 536 1000 (ask for on-call virologist)
Email: [email protected]
Orkney 01856 888217
Shetland 015950 743011
Tayside 01382 632559
Western Isles 01851 708033
Ayrshire & Arran 01563 827420